From 5781e1c67a4eb27f0bd82a0476820fb16e8d3d2d Mon Sep 17 00:00:00 2001
From: Thomas Witkowski <thomas.witkowski@gmx.de>
Date: Tue, 28 Jul 2009 07:44:52 +0000
Subject: [PATCH] Added --with-petsc parameter to automake system.

---
 AMDiS/Makefile.in               |   1 +
 AMDiS/bin/Makefile.am           |   3 +-
 AMDiS/bin/Makefile.in           |   4 +-
 AMDiS/configure                 |  71 ++++++----
 AMDiS/configure.ac              |   3 +
 AMDiS/src/DOFMatrix.h           |   8 +-
 AMDiS/src/ParallelDomainBase.cc | 240 +++++---------------------------
 AMDiS/src/ParallelDomainVec.cc  |   2 +-
 AMDiS/src/ProblemVec.cc         |  22 ++-
 9 files changed, 102 insertions(+), 252 deletions(-)

diff --git a/AMDiS/Makefile.in b/AMDiS/Makefile.in
index 056838fe..e7566807 100644
--- a/AMDiS/Makefile.in
+++ b/AMDiS/Makefile.in
@@ -138,6 +138,7 @@ PACKAGE_STRING = @PACKAGE_STRING@
 PACKAGE_TARNAME = @PACKAGE_TARNAME@
 PACKAGE_VERSION = @PACKAGE_VERSION@
 PATH_SEPARATOR = @PATH_SEPARATOR@
+PETSC_DIR = @PETSC_DIR@
 RANLIB = @RANLIB@
 SED = @SED@
 SET_MAKE = @SET_MAKE@
diff --git a/AMDiS/bin/Makefile.am b/AMDiS/bin/Makefile.am
index 6fe348bc..a6a74172 100644
--- a/AMDiS/bin/Makefile.am
+++ b/AMDiS/bin/Makefile.am
@@ -33,8 +33,7 @@ if USE_PARALLEL_DOMAIN_AMDIS
   $(PARALLEL_DIR)/ParallelDomainScal.h $(PARALLEL_DIR)/ParallelDomainScal.cc \
   $(PARALLEL_DIR)/ParallelDomainVec.h $(PARALLEL_DIR)/ParallelDomainVec.cc
   libamdis_la_CXXFLAGS += -DHAVE_PARALLEL_DOMAIN_AMDIS=1
-#  AMDIS_INCLUDES += -I/work/home7/witkowsk/local/include
-  AMDIS_INCLUDES += -I/u/witkowski/local/petsc-3.0.0-p4/include -I/u/witkowski/local/petsc-3.0.0-p4/linux-gnu-c-debug/include
+  AMDIS_INCLUDES += -I$(PETSC_DIR)/include -I$(PETSC_DIR)/$(PETSC_ARCH)/include
 endif
 
 if ENABLE_UMFPACK
diff --git a/AMDiS/bin/Makefile.in b/AMDiS/bin/Makefile.in
index 79f9d24e..aace53f9 100644
--- a/AMDiS/bin/Makefile.in
+++ b/AMDiS/bin/Makefile.in
@@ -43,8 +43,7 @@ host_triplet = @host@
 @USE_PARALLEL_DOMAIN_AMDIS_TRUE@  $(PARALLEL_DIR)/ParallelDomainVec.h $(PARALLEL_DIR)/ParallelDomainVec.cc
 
 @USE_PARALLEL_DOMAIN_AMDIS_TRUE@am__append_3 = -DHAVE_PARALLEL_DOMAIN_AMDIS=1
-#  AMDIS_INCLUDES += -I/work/home7/witkowsk/local/include
-@USE_PARALLEL_DOMAIN_AMDIS_TRUE@am__append_4 = -I/u/witkowski/local/petsc-3.0.0-p4/include -I/u/witkowski/local/petsc-3.0.0-p4/linux-gnu-c-debug/include
+@USE_PARALLEL_DOMAIN_AMDIS_TRUE@am__append_4 = -I$(PETSC_DIR)/include -I$(PETSC_DIR)/$(PETSC_ARCH)/include
 @ENABLE_UMFPACK_TRUE@am__append_5 = -DHAVE_UMFPACK=1 -DMTL_HAS_UMFPACK
 @ENABLE_UMFPACK_TRUE@am__append_6 = -I$(LIB_DIR)/UFconfig \
 @ENABLE_UMFPACK_TRUE@	            -I$(LIB_DIR)/AMD/Include \
@@ -395,6 +394,7 @@ PACKAGE_STRING = @PACKAGE_STRING@
 PACKAGE_TARNAME = @PACKAGE_TARNAME@
 PACKAGE_VERSION = @PACKAGE_VERSION@
 PATH_SEPARATOR = @PATH_SEPARATOR@
+PETSC_DIR = @PETSC_DIR@
 RANLIB = @RANLIB@
 SED = @SED@
 SET_MAKE = @SET_MAKE@
diff --git a/AMDiS/configure b/AMDiS/configure
index f9cd175d..4196f21b 100755
--- a/AMDiS/configure
+++ b/AMDiS/configure
@@ -462,7 +462,7 @@ ac_includes_default="\
 # include <unistd.h>
 #endif"
 
-ac_subst_vars='SHELL PATH_SEPARATOR PACKAGE_NAME PACKAGE_TARNAME PACKAGE_VERSION PACKAGE_STRING PACKAGE_BUGREPORT exec_prefix prefix program_transform_name bindir sbindir libexecdir datadir sysconfdir sharedstatedir localstatedir libdir includedir oldincludedir infodir mandir build_alias host_alias target_alias DEFS ECHO_C ECHO_N ECHO_T LIBS INSTALL_PROGRAM INSTALL_SCRIPT INSTALL_DATA CYGPATH_W PACKAGE VERSION ACLOCAL AUTOCONF AUTOMAKE AUTOHEADER MAKEINFO install_sh STRIP ac_ct_STRIP INSTALL_STRIP_PROGRAM mkdir_p AWK SET_MAKE am__leading_dot AMTAR am__tar am__untar MAINTAINER_MODE_TRUE MAINTAINER_MODE_FALSE MAINT AMDIS_DEBUG_TRUE AMDIS_DEBUG_FALSE CXX CC AMDIS_INTEL_TRUE AMDIS_INTEL_FALSE AMDIS_OPENMP_TRUE AMDIS_OPENMP_FALSE OPENMP_FLAG MPI_DIR USE_PARALLEL_AMDIS_TRUE USE_PARALLEL_AMDIS_FALSE USE_PARALLEL_DOMAIN_AMDIS_TRUE USE_PARALLEL_DOMAIN_AMDIS_FALSE ENABLE_UMFPACK_TRUE ENABLE_UMFPACK_FALSE ENABLE_MKL_TRUE ENABLE_MKL_FALSE DUNE_DIR ENABLE_DUNE_TRUE ENABLE_DUNE_FALSE ENABLE_BOOST_TRUE ENABLE_BOOST_FALSE CFLAGS LDFLAGS CPPFLAGS ac_ct_CC EXEEXT OBJEXT DEPDIR am__include am__quote AMDEP_TRUE AMDEP_FALSE AMDEPBACKSLASH CCDEPMODE am__fastdepCC_TRUE am__fastdepCC_FALSE CXXFLAGS ac_ct_CXX CXXDEPMODE am__fastdepCXX_TRUE am__fastdepCXX_FALSE build build_cpu build_vendor build_os host host_cpu host_vendor host_os SED EGREP LN_S ECHO AR ac_ct_AR RANLIB ac_ct_RANLIB CPP CXXCPP F77 FFLAGS ac_ct_F77 LIBTOOL LIBOBJS LTLIBOBJS'
+ac_subst_vars='SHELL PATH_SEPARATOR PACKAGE_NAME PACKAGE_TARNAME PACKAGE_VERSION PACKAGE_STRING PACKAGE_BUGREPORT exec_prefix prefix program_transform_name bindir sbindir libexecdir datadir sysconfdir sharedstatedir localstatedir libdir includedir oldincludedir infodir mandir build_alias host_alias target_alias DEFS ECHO_C ECHO_N ECHO_T LIBS INSTALL_PROGRAM INSTALL_SCRIPT INSTALL_DATA CYGPATH_W PACKAGE VERSION ACLOCAL AUTOCONF AUTOMAKE AUTOHEADER MAKEINFO install_sh STRIP ac_ct_STRIP INSTALL_STRIP_PROGRAM mkdir_p AWK SET_MAKE am__leading_dot AMTAR am__tar am__untar MAINTAINER_MODE_TRUE MAINTAINER_MODE_FALSE MAINT AMDIS_DEBUG_TRUE AMDIS_DEBUG_FALSE CXX CC AMDIS_INTEL_TRUE AMDIS_INTEL_FALSE AMDIS_OPENMP_TRUE AMDIS_OPENMP_FALSE OPENMP_FLAG MPI_DIR PETSC_DIR USE_PARALLEL_AMDIS_TRUE USE_PARALLEL_AMDIS_FALSE USE_PARALLEL_DOMAIN_AMDIS_TRUE USE_PARALLEL_DOMAIN_AMDIS_FALSE ENABLE_UMFPACK_TRUE ENABLE_UMFPACK_FALSE ENABLE_MKL_TRUE ENABLE_MKL_FALSE DUNE_DIR ENABLE_DUNE_TRUE ENABLE_DUNE_FALSE ENABLE_BOOST_TRUE ENABLE_BOOST_FALSE CFLAGS LDFLAGS CPPFLAGS ac_ct_CC EXEEXT OBJEXT DEPDIR am__include am__quote AMDEP_TRUE AMDEP_FALSE AMDEPBACKSLASH CCDEPMODE am__fastdepCC_TRUE am__fastdepCC_FALSE CXXFLAGS ac_ct_CXX CXXDEPMODE am__fastdepCXX_TRUE am__fastdepCXX_FALSE build build_cpu build_vendor build_os host host_cpu host_vendor host_os SED EGREP LN_S ECHO AR ac_ct_AR RANLIB ac_ct_RANLIB CPP CXXCPP F77 FFLAGS ac_ct_F77 LIBTOOL LIBOBJS LTLIBOBJS'
 ac_subst_files=''
 
 # Initialize some variables set by options.
@@ -1046,6 +1046,7 @@ Optional Packages:
   --with-PACKAGE[=ARG]    use PACKAGE [ARG=yes]
   --without-PACKAGE       do not use PACKAGE (same as --with-PACKAGE=no)
   --with-mpi=MPI_DIR
+  --with-petsc=PETSC_DIR
   --with-dune=DUNE_DIR
   --with-gnu-ld           assume the C compiler uses GNU ld [default=no]
   --with-pic              try to use only PIC/non-PIC objects [default=use
@@ -2078,6 +2079,17 @@ if test $mpidir != no ; then
 
 fi
 
+
+# Check whether --with-petsc or --without-petsc was given.
+if test "${with_petsc+set}" = set; then
+  withval="$with_petsc"
+  petscdir=$withval
+else
+  petscdir=no
+fi;
+PETSC_DIR=$petscdir
+
+
 # Check whether --enable-parmetis or --disable-parmetis was given.
 if test "${enable_parmetis+set}" = set; then
   enableval="$enable_parmetis"
@@ -4410,7 +4422,7 @@ ia64-*-hpux*)
   ;;
 *-*-irix6*)
   # Find out which ABI we are using.
-  echo '#line 4413 "configure"' > conftest.$ac_ext
+  echo '#line 4425 "configure"' > conftest.$ac_ext
   if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5
   (eval $ac_compile) 2>&5
   ac_status=$?
@@ -5545,7 +5557,7 @@ fi
 
 
 # Provide some information about the compiler.
-echo "$as_me:5548:" \
+echo "$as_me:5560:" \
      "checking for Fortran 77 compiler version" >&5
 ac_compiler=`set X $ac_compile; echo $2`
 { (eval echo "$as_me:$LINENO: \"$ac_compiler --version </dev/null >&5\"") >&5
@@ -6608,11 +6620,11 @@ else
    -e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; t' \
    -e 's: [^ ]*conftest\.: $lt_compiler_flag&:; t' \
    -e 's:$: $lt_compiler_flag:'`
-   (eval echo "\"\$as_me:6611: $lt_compile\"" >&5)
+   (eval echo "\"\$as_me:6623: $lt_compile\"" >&5)
    (eval "$lt_compile" 2>conftest.err)
    ac_status=$?
    cat conftest.err >&5
-   echo "$as_me:6615: \$? = $ac_status" >&5
+   echo "$as_me:6627: \$? = $ac_status" >&5
    if (exit $ac_status) && test -s "$ac_outfile"; then
      # The compiler can only warn and ignore the option if not recognized
      # So say no if there are warnings other than the usual output.
@@ -6876,11 +6888,11 @@ else
    -e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; t' \
    -e 's: [^ ]*conftest\.: $lt_compiler_flag&:; t' \
    -e 's:$: $lt_compiler_flag:'`
-   (eval echo "\"\$as_me:6879: $lt_compile\"" >&5)
+   (eval echo "\"\$as_me:6891: $lt_compile\"" >&5)
    (eval "$lt_compile" 2>conftest.err)
    ac_status=$?
    cat conftest.err >&5
-   echo "$as_me:6883: \$? = $ac_status" >&5
+   echo "$as_me:6895: \$? = $ac_status" >&5
    if (exit $ac_status) && test -s "$ac_outfile"; then
      # The compiler can only warn and ignore the option if not recognized
      # So say no if there are warnings other than the usual output.
@@ -6980,11 +6992,11 @@ else
    -e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; t' \
    -e 's: [^ ]*conftest\.: $lt_compiler_flag&:; t' \
    -e 's:$: $lt_compiler_flag:'`
-   (eval echo "\"\$as_me:6983: $lt_compile\"" >&5)
+   (eval echo "\"\$as_me:6995: $lt_compile\"" >&5)
    (eval "$lt_compile" 2>out/conftest.err)
    ac_status=$?
    cat out/conftest.err >&5
-   echo "$as_me:6987: \$? = $ac_status" >&5
+   echo "$as_me:6999: \$? = $ac_status" >&5
    if (exit $ac_status) && test -s out/conftest2.$ac_objext
    then
      # The compiler can only warn and ignore the option if not recognized
@@ -8449,7 +8461,7 @@ linux*)
   libsuff=
   case "$host_cpu" in
   x86_64*|s390x*|powerpc64*)
-    echo '#line 8452 "configure"' > conftest.$ac_ext
+    echo '#line 8464 "configure"' > conftest.$ac_ext
     if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5
   (eval $ac_compile) 2>&5
   ac_status=$?
@@ -9346,7 +9358,7 @@ else
   lt_dlunknown=0; lt_dlno_uscore=1; lt_dlneed_uscore=2
   lt_status=$lt_dlunknown
   cat > conftest.$ac_ext <<EOF
-#line 9349 "configure"
+#line 9361 "configure"
 #include "confdefs.h"
 
 #if HAVE_DLFCN_H
@@ -9446,7 +9458,7 @@ else
   lt_dlunknown=0; lt_dlno_uscore=1; lt_dlneed_uscore=2
   lt_status=$lt_dlunknown
   cat > conftest.$ac_ext <<EOF
-#line 9449 "configure"
+#line 9461 "configure"
 #include "confdefs.h"
 
 #if HAVE_DLFCN_H
@@ -11789,11 +11801,11 @@ else
    -e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; t' \
    -e 's: [^ ]*conftest\.: $lt_compiler_flag&:; t' \
    -e 's:$: $lt_compiler_flag:'`
-   (eval echo "\"\$as_me:11792: $lt_compile\"" >&5)
+   (eval echo "\"\$as_me:11804: $lt_compile\"" >&5)
    (eval "$lt_compile" 2>conftest.err)
    ac_status=$?
    cat conftest.err >&5
-   echo "$as_me:11796: \$? = $ac_status" >&5
+   echo "$as_me:11808: \$? = $ac_status" >&5
    if (exit $ac_status) && test -s "$ac_outfile"; then
      # The compiler can only warn and ignore the option if not recognized
      # So say no if there are warnings other than the usual output.
@@ -11893,11 +11905,11 @@ else
    -e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; t' \
    -e 's: [^ ]*conftest\.: $lt_compiler_flag&:; t' \
    -e 's:$: $lt_compiler_flag:'`
-   (eval echo "\"\$as_me:11896: $lt_compile\"" >&5)
+   (eval echo "\"\$as_me:11908: $lt_compile\"" >&5)
    (eval "$lt_compile" 2>out/conftest.err)
    ac_status=$?
    cat out/conftest.err >&5
-   echo "$as_me:11900: \$? = $ac_status" >&5
+   echo "$as_me:11912: \$? = $ac_status" >&5
    if (exit $ac_status) && test -s out/conftest2.$ac_objext
    then
      # The compiler can only warn and ignore the option if not recognized
@@ -12429,7 +12441,7 @@ linux*)
   libsuff=
   case "$host_cpu" in
   x86_64*|s390x*|powerpc64*)
-    echo '#line 12432 "configure"' > conftest.$ac_ext
+    echo '#line 12444 "configure"' > conftest.$ac_ext
     if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5
   (eval $ac_compile) 2>&5
   ac_status=$?
@@ -13487,11 +13499,11 @@ else
    -e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; t' \
    -e 's: [^ ]*conftest\.: $lt_compiler_flag&:; t' \
    -e 's:$: $lt_compiler_flag:'`
-   (eval echo "\"\$as_me:13490: $lt_compile\"" >&5)
+   (eval echo "\"\$as_me:13502: $lt_compile\"" >&5)
    (eval "$lt_compile" 2>conftest.err)
    ac_status=$?
    cat conftest.err >&5
-   echo "$as_me:13494: \$? = $ac_status" >&5
+   echo "$as_me:13506: \$? = $ac_status" >&5
    if (exit $ac_status) && test -s "$ac_outfile"; then
      # The compiler can only warn and ignore the option if not recognized
      # So say no if there are warnings other than the usual output.
@@ -13591,11 +13603,11 @@ else
    -e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; t' \
    -e 's: [^ ]*conftest\.: $lt_compiler_flag&:; t' \
    -e 's:$: $lt_compiler_flag:'`
-   (eval echo "\"\$as_me:13594: $lt_compile\"" >&5)
+   (eval echo "\"\$as_me:13606: $lt_compile\"" >&5)
    (eval "$lt_compile" 2>out/conftest.err)
    ac_status=$?
    cat out/conftest.err >&5
-   echo "$as_me:13598: \$? = $ac_status" >&5
+   echo "$as_me:13610: \$? = $ac_status" >&5
    if (exit $ac_status) && test -s out/conftest2.$ac_objext
    then
      # The compiler can only warn and ignore the option if not recognized
@@ -15040,7 +15052,7 @@ linux*)
   libsuff=
   case "$host_cpu" in
   x86_64*|s390x*|powerpc64*)
-    echo '#line 15043 "configure"' > conftest.$ac_ext
+    echo '#line 15055 "configure"' > conftest.$ac_ext
     if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5
   (eval $ac_compile) 2>&5
   ac_status=$?
@@ -15818,11 +15830,11 @@ else
    -e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; t' \
    -e 's: [^ ]*conftest\.: $lt_compiler_flag&:; t' \
    -e 's:$: $lt_compiler_flag:'`
-   (eval echo "\"\$as_me:15821: $lt_compile\"" >&5)
+   (eval echo "\"\$as_me:15833: $lt_compile\"" >&5)
    (eval "$lt_compile" 2>conftest.err)
    ac_status=$?
    cat conftest.err >&5
-   echo "$as_me:15825: \$? = $ac_status" >&5
+   echo "$as_me:15837: \$? = $ac_status" >&5
    if (exit $ac_status) && test -s "$ac_outfile"; then
      # The compiler can only warn and ignore the option if not recognized
      # So say no if there are warnings other than the usual output.
@@ -16086,11 +16098,11 @@ else
    -e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; t' \
    -e 's: [^ ]*conftest\.: $lt_compiler_flag&:; t' \
    -e 's:$: $lt_compiler_flag:'`
-   (eval echo "\"\$as_me:16089: $lt_compile\"" >&5)
+   (eval echo "\"\$as_me:16101: $lt_compile\"" >&5)
    (eval "$lt_compile" 2>conftest.err)
    ac_status=$?
    cat conftest.err >&5
-   echo "$as_me:16093: \$? = $ac_status" >&5
+   echo "$as_me:16105: \$? = $ac_status" >&5
    if (exit $ac_status) && test -s "$ac_outfile"; then
      # The compiler can only warn and ignore the option if not recognized
      # So say no if there are warnings other than the usual output.
@@ -16190,11 +16202,11 @@ else
    -e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; t' \
    -e 's: [^ ]*conftest\.: $lt_compiler_flag&:; t' \
    -e 's:$: $lt_compiler_flag:'`
-   (eval echo "\"\$as_me:16193: $lt_compile\"" >&5)
+   (eval echo "\"\$as_me:16205: $lt_compile\"" >&5)
    (eval "$lt_compile" 2>out/conftest.err)
    ac_status=$?
    cat out/conftest.err >&5
-   echo "$as_me:16197: \$? = $ac_status" >&5
+   echo "$as_me:16209: \$? = $ac_status" >&5
    if (exit $ac_status) && test -s out/conftest2.$ac_objext
    then
      # The compiler can only warn and ignore the option if not recognized
@@ -17659,7 +17671,7 @@ linux*)
   libsuff=
   case "$host_cpu" in
   x86_64*|s390x*|powerpc64*)
-    echo '#line 17662 "configure"' > conftest.$ac_ext
+    echo '#line 17674 "configure"' > conftest.$ac_ext
     if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5
   (eval $ac_compile) 2>&5
   ac_status=$?
@@ -19661,6 +19673,7 @@ s,@AMDIS_OPENMP_TRUE@,$AMDIS_OPENMP_TRUE,;t t
 s,@AMDIS_OPENMP_FALSE@,$AMDIS_OPENMP_FALSE,;t t
 s,@OPENMP_FLAG@,$OPENMP_FLAG,;t t
 s,@MPI_DIR@,$MPI_DIR,;t t
+s,@PETSC_DIR@,$PETSC_DIR,;t t
 s,@USE_PARALLEL_AMDIS_TRUE@,$USE_PARALLEL_AMDIS_TRUE,;t t
 s,@USE_PARALLEL_AMDIS_FALSE@,$USE_PARALLEL_AMDIS_FALSE,;t t
 s,@USE_PARALLEL_DOMAIN_AMDIS_TRUE@,$USE_PARALLEL_DOMAIN_AMDIS_TRUE,;t t
diff --git a/AMDiS/configure.ac b/AMDiS/configure.ac
index f03e2bd5..192f423f 100644
--- a/AMDiS/configure.ac
+++ b/AMDiS/configure.ac
@@ -54,6 +54,9 @@ if test $mpidir != no ; then
   AC_SUBST(CC, $mpidir/bin/mpicc)
 fi
 
+AC_ARG_WITH(petsc, [  --with-petsc=PETSC_DIR], petscdir=$withval, petscdir=no)
+AC_SUBST(PETSC_DIR, $petscdir)
+
 AC_ARG_ENABLE(parmetis,
   [  --enable-parmetis   Compile with the ParMetis library],
   [case "${enableval}" in
diff --git a/AMDiS/src/DOFMatrix.h b/AMDiS/src/DOFMatrix.h
index b26fdd0e..5ae24aa9 100644
--- a/AMDiS/src/DOFMatrix.h
+++ b/AMDiS/src/DOFMatrix.h
@@ -256,12 +256,14 @@ namespace AMDiS {
     }
 
     /** \brief
-     *  Finishes insertion. For compressed matrix types, this is where the 
-     *  compression happens.
+     * Finishes insertion. For compressed matrix types, this is where the 
+     * compression happens.
      */
     void finishInsertion()
     {
-      TEST_EXIT(inserter)("Inserter wasn't used or is already finished.");
+      FUNCNAME("DOFMatrix::finishInsertion()");
+
+      TEST_EXIT(inserter)("Inserter wasn't used or is already finished.\n");
       
       delete inserter;
       inserter= 0;
diff --git a/AMDiS/src/ParallelDomainBase.cc b/AMDiS/src/ParallelDomainBase.cc
index 5bcb5022..68b3ad19 100644
--- a/AMDiS/src/ParallelDomainBase.cc
+++ b/AMDiS/src/ParallelDomainBase.cc
@@ -67,23 +67,6 @@ namespace AMDiS {
     if (mpiSize <= 1)
       return;
 
-#if 0
-    if (mpiRank == 0) {
-      std::map<int, double> vec;
-      
-      TraverseStack stack;
-      ElInfo *elInfo = stack.traverseFirst(mesh, -1,
-					   Mesh::CALL_LEAF_EL | Mesh::FILL_NEIGH);
-      while (elInfo) {
-	vec[elInfo->getElement()->getIndex()] = static_cast<double>(elInfo->getElement()->getIndex());
-	elInfo = stack.traverseNext(elInfo);
-      }
-
-      ElementFileWriter::writeFile(vec, feSpace, "test.vtu");
-    }
-#endif
-
-
     // Test, if the mesh is the macro mesh only! Paritioning of the mesh is supported
     // only for macro meshes, so it will not work yet if the mesh is already refined
     // in some way.
@@ -130,23 +113,6 @@ namespace AMDiS {
 
     updateDofAdmins();
 
-#if 0
-    if (mpiRank == 0) {
-      TraverseStack stack;
-      ElInfo *elInfo = stack.traverseFirst(mesh, -1, Mesh::CALL_LEAF_EL);
-      while (elInfo) {
-	if (elInfo->getElement()->getIndex() == 4) {
-	  WorldVector<double> x;
-	  mesh->getDofIndexCoords(elInfo->getElement()->getDOF(0), feSpace, x);
-	  std::cout << "FOUND!" << std::endl;
-	  x.print();
-	}
-
-	elInfo = stack.traverseNext(elInfo);
-      }
-    }
-#endif
-
 
     // === Global refinements. ===
 
@@ -317,7 +283,7 @@ namespace AMDiS {
 
     clock_t first = clock();
 
-    using mtl::tag::major; using mtl::tag::nz; using mtl::begin; using mtl::end;
+    using mtl::tag::row; using mtl::tag::nz; using mtl::begin; using mtl::end;
     namespace traits= mtl::traits;
     typedef DOFMatrix::base_matrix_type Matrix;
 
@@ -334,32 +300,32 @@ namespace AMDiS {
  	if ((*mat)[i][j]) {
 	  Matrix bmat = (*mat)[i][j]->getBaseMatrix();
 
-	  traits::row<Matrix>::type row(bmat);
 	  traits::col<Matrix>::type col(bmat);
 	  traits::const_value<Matrix>::type value(bmat);
 	  
-	  typedef traits::range_generator<major, Matrix>::type cursor_type;
+	  typedef traits::range_generator<row, Matrix>::type cursor_type;
 	  typedef traits::range_generator<nz, cursor_type>::type icursor_type;
 	  
-	  for (cursor_type cursor = begin<major>(bmat), 
-		 cend = end<major>(bmat); cursor != cend; ++cursor) {
+	  for (cursor_type cursor = begin<row>(bmat), 
+		 cend = end<row>(bmat); cursor != cend; ++cursor) {
+
+	    int r = mapLocalGlobalDOFs[*cursor] * nComponents + i;
+	    r -= rstart * nComponents;
+
+	    if (r >= nRankRows)
+	      continue;
+	      
 	    for (icursor_type icursor = begin<nz>(cursor), 
 		   icend = end<nz>(cursor); icursor != icend; ++icursor)
 	      if (value(*icursor) != 0.0) {
-		int r = mapLocalGlobalDOFs[row(*icursor)] * nComponents + i;
-		r -= rstart * nComponents;
-
 		int c = mapLocalGlobalDOFs[col(*icursor)] * nComponents + j;
 
-		if (r < nRankRows) {
-
-		  if (c >= rstart * nComponents && 
-		      c < rstart * nComponents + nRankRows)
-		    d_nnz[r]++;
-		  else
-		    o_nnz[r]++;		  
-		}
-	      }
+		if (c >= rstart * nComponents && 
+		    c < rstart * nComponents + nRankRows)
+		  d_nnz[r]++;
+		else
+		  o_nnz[r]++;		  
+	      }    
 	  }
 	}
 
@@ -389,6 +355,9 @@ namespace AMDiS {
     for (int i = 0; i < nComponents; i++)
       setDofVector(vec->getDOFVector(i), nComponents, i);
 
+    VecAssemblyBegin(petscRhsVec);
+    VecAssemblyEnd(petscRhsVec);
+
     INFO(info, 8)("Fill petsc matrix needed %.5f seconds\n", TIME_USED(first, clock()));
   }
 
@@ -401,7 +370,7 @@ namespace AMDiS {
     PC pc;
 
     KSPCreate(PETSC_COMM_WORLD, &ksp);
-    KSPSetOperators(ksp, petscMatrix, petscMatrix, DIFFERENT_NONZERO_PATTERN);
+    KSPSetOperators(ksp, petscMatrix, petscMatrix, SAME_NONZERO_PATTERN);
     KSPGetPC(ksp, &pc);
     //PCSetType(pc, PCJACOBI);
     PCSetType(pc, PCILU);
@@ -471,17 +440,21 @@ namespace AMDiS {
   {
     FUNCNAME("ParallelDomainBase::solvePetscMatrix()");
 
-    KSP ksp;
+    KSP solver;
     PC pc;
 
-    KSPCreate(PETSC_COMM_WORLD, &ksp);
-    KSPSetOperators(ksp, petscMatrix, petscMatrix, DIFFERENT_NONZERO_PATTERN);
-    KSPGetPC(ksp, &pc);
+    KSPCreate(PETSC_COMM_WORLD, &solver);
+    KSPSetOperators(solver, petscMatrix, petscMatrix, SAME_NONZERO_PATTERN); 
+
+    KSPSetTolerances(solver, 1.e-8, PETSC_DEFAULT, PETSC_DEFAULT, PETSC_DEFAULT);
+    KSPSetType(solver, KSPBCGS);
+    KSPMonitorSet(solver, myKSPMonitor, PETSC_NULL, 0);
+
+    KSPGetPC(solver, &pc);
     PCSetType(pc, PCKSP);
-    KSPSetTolerances(ksp, 1.e-8, PETSC_DEFAULT, PETSC_DEFAULT, PETSC_DEFAULT);
-    KSPSetType(ksp, KSPBCGS);
-    KSPMonitorSet(ksp, myKSPMonitor, PETSC_NULL, 0);
-    KSPSolve(ksp, petscRhsVec, petscSolVec);
+
+    KSPSetUp(solver);
+    KSPSolve(solver, petscRhsVec, petscSolVec);
 
     PetscScalar *vecPointer;
     VecGetArray(petscSolVec, &vecPointer);
@@ -550,6 +523,8 @@ namespace AMDiS {
       delete [] sendBuffers[i];
 
     MatDestroy(petscMatrix);
+    PCDestroy(pc);
+    KSPDestroy(solver);
   }
 
 
@@ -655,24 +630,6 @@ namespace AMDiS {
 	    bool isRankDOF2 = (find(rankDOFs.begin(), rankDOFs.end(), boundDOF2) != rankDOFs.end());
 	    bool ranksBoundary = isRankDOF1 || isRankDOF2;
 
-#if 0
-	    if (mpiRank == 3 && ranksBoundary && 
-		partitionVec[elInfo->getNeighbour(i)->getIndex()] == 2) {
-	      std::cout << "ADD MY BOUND " << element->getIndex() << "/" << i 
-			<< "  with  " 
-			<< elInfo->getNeighbour(i)->getIndex() << "/"
-			<< elInfo->getSideOfNeighbour(i) << std::endl;
-	    }
-
-	    if (mpiRank == 2 && !ranksBoundary && 
-		partitionVec[elInfo->getNeighbour(i)->getIndex()] == 3) {
-	      std::cout << "ADD OT BOUND " << element->getIndex() << "/" << i 
-			<< "  with  " 
-			<< elInfo->getNeighbour(i)->getIndex() << "/"
-			<< elInfo->getSideOfNeighbour(i) << std::endl;
-	    }
-#endif
-
 	    // === And add the part of the interior boundary. ===
 
 	    AtomicBoundary& bound = 
@@ -832,15 +789,6 @@ namespace AMDiS {
     for (DofContainer::iterator dofIt = rankAllDofs.begin();
 	 dofIt != rankAllDofs.end(); ++dofIt) {
 
-#if 0
-      if (mpiRank == 0) {
-	std::cout << "COORDs of dof = " << i << std::endl;
-	WorldVector<double> x;
-	mesh->getDofIndexCoords(*dofIt, feSpace, x);
-	x.print();	
-      }
-#endif
-
       rankDofsNewLocalIndex[*dofIt] = i;
       // First, we set all dofs in ranks partition to be owend by the rank. Later,
       // the dofs in ranks partition that are owned by other rank are set to false.
@@ -930,11 +878,6 @@ namespace AMDiS {
 	sendBuffers[i][c++] = *(dofIt->first);
 	sendBuffers[i][c++] = dofIt->second;
 
-#if 0
-	if (mpiRank == 3 && sendIt->first == 2)
-	  std::cout << "SEND DOF: " << dofIt->first << std::endl;
-#endif
-
 	sendDofs[sendIt->first].push_back(dofIt->first);
       }
 
@@ -997,11 +940,6 @@ namespace AMDiS {
 	  if (*(dofIt->first) == oldDof && !dofChanged[dofIt->first]) {
 	    dofChanged[dofIt->first] = true;
 
-#if 0
-	    if (mpiRank == 2 && recvIt->first == 3)
-	      std::cout << "RECV DOF: " << dofIt->first << std::endl;
-#endif
-	
 	    recvDofs[recvIt->first].push_back(dofIt->first);
 	    rankDofsNewGlobalIndex[dofIt->first] = newGlobalDof;
 	    isRankDof[rankDofsNewLocalIndex[dofIt->first]] = false;
@@ -1065,16 +1003,6 @@ namespace AMDiS {
       for (std::vector<AtomicBoundary>::iterator boundIt = it->second.begin();
 	   boundIt != it->second.end(); ++boundIt) {
 
-#if 0
-	if (mpiRank == 3 && it->first == 2) 
-	  std::cout << "GO ON MY BOUND: " << boundIt->rankObject.elIndex 
-		    << "/" << boundIt->rankObject.ithObjAtBoundary << " with "
-		    << boundIt->neighbourObject.elIndex << "/"
-		    << boundIt->neighbourObject.ithObjAtBoundary
-		    << std::endl;
-#endif
-
-
 	DofContainer dofs;
 	DofContainer &dofsToSend = sendDofs[it->first];
 
@@ -1095,17 +1023,6 @@ namespace AMDiS {
 	  ERROR_EXIT("Should never happen!\n");
 	}
 
-#if 0
-	if (mpiRank == 3 && it->first == 2) {
-	  WorldVector<double> x;
-	  mesh->getDofIndexCoords(dofs[0], feSpace, x);
-	  x.print();
-	  mesh->getDofIndexCoords(dofs[1], feSpace, x);
-	  x.print();
-	}
-#endif
-	
-
 	for (DofContainer::iterator dofIt = dofs.begin(); dofIt != dofs.end(); ++dofIt)
 	  if (find(dofsToSend.begin(), dofsToSend.end(), *dofIt) == dofsToSend.end())
 	    dofsToSend.push_back(*dofIt);	
@@ -1128,16 +1045,6 @@ namespace AMDiS {
       for (std::vector<AtomicBoundary>::iterator boundIt = it->second.begin();
 	   boundIt != it->second.end(); ++boundIt) {
 
-#if 0
-	if (mpiRank == 2 && it->first == 3) 
-	  std::cout << "GO ON OT BOUND: " << boundIt->rankObject.elIndex 
-		    << "/" << boundIt->rankObject.ithObjAtBoundary << " with "
-		    << boundIt->neighbourObject.elIndex << "/"
-		    << boundIt->neighbourObject.ithObjAtBoundary
-		    << std::endl;
-#endif
-
-
 	DofContainer dofs;
 	DofContainer &dofsToRecv = recvDofs[it->first];
 
@@ -1168,16 +1075,6 @@ namespace AMDiS {
 	  ERROR_EXIT("Should never happen!\n");
 	}
 
-#if 0
-	if (mpiRank == 2 && it->first == 3) {
-	  WorldVector<double> x;
-	  mesh->getDofIndexCoords(dofs[0], feSpace, x);
-	  x.print();
-	  mesh->getDofIndexCoords(dofs[1], feSpace, x);
-	  x.print();
-	}
-#endif
-
 	for (DofContainer::iterator dofIt = dofs.begin(); dofIt != dofs.end(); ++dofIt) {
 	  DofContainer::iterator eraseIt = find(rankDOFs.begin(), rankDOFs.end(), *dofIt);
 	  if (eraseIt != rankDOFs.end())
@@ -1547,22 +1444,9 @@ namespace AMDiS {
 
       int nSendInt = rankIt->second.size();
       int* buffer = new int[nSendInt];
-      for (int i = 0; i < nSendInt; i++) {
-
-#if 0
-	if (mpiRank == 3 && rankIt->first == 2) {
-	  std::cout << "MY BOUND: " << (rankIt->second)[i].rankObject.elIndex
-		    << "/" << (rankIt->second)[i].rankObject.ithObjAtBoundary
-		    << "  with neig " 
-		    << (rankIt->second)[i].neighbourObject.elIndex
-		    << "/" << (rankIt->second)[i].neighbourObject.ithObjAtBoundary
-		    << std::endl;
-	}
-#endif
-
-
+      for (int i = 0; i < nSendInt; i++)
 	buffer[i] = (rankIt->second)[i].rankObject.elIndex;
-      }
+      
       sendBuffers.push_back(buffer);
       
       request[requestCounter++] =
@@ -1593,20 +1477,6 @@ namespace AMDiS {
 	("Boundaries does not fit together!\n");      
 
       for (int i = 0; i < static_cast<int>(rankIt->second.size()); i++) {
-
-#if 0
-	if (mpiRank == 2 && rankIt->first == 3) {
-	  std::cout << "OT BOUND: " << (rankIt->second)[i].rankObject.elIndex
-		    << "/" << (rankIt->second)[i].rankObject.ithObjAtBoundary
-		    << "  with neig " 
-		    << (rankIt->second)[i].neighbourObject.elIndex
-		    << "/" << (rankIt->second)[i].neighbourObject.ithObjAtBoundary
-		    << std::endl;
-	}
-
-#endif
-
-
 	int elIndex1 = recvBuffers[bufCounter][i];
 	int elIndex2 = otherIntBoundary.boundary[rankIt->first][i].neighbourObject.elIndex;
 
@@ -1622,27 +1492,6 @@ namespace AMDiS {
   {
     FUNCNAME("ParallelDomainBase::DbgTestCommonDofs()");
 
-
-#if 0
-    {
-      TraverseStack stack;
-      ElInfo *elInfo = stack.traverseFirst(mesh, -1, Mesh::CALL_EVERY_EL_PREORDER);
-      while (elInfo) {
-	Element *el = elInfo->getElement();
-	for (int i = 0; i < 3; i++) {
-	  if (mpiRank == 2 && el->getDOF(i, 0) == 3) 
-	    std::cout << "RANK 2 EL = " << el->getIndex() << " i = " << i << std::endl;
-
-	  if (mpiRank == 3 && el->getDOF(i, 0) == 4) 
-	    std::cout << "RANK 3 EL = " << el->getIndex() << " i = " << i << std::endl;
-
-	}
-
-	elInfo = stack.traverseNext(elInfo);
-      }
-    }
-#endif
-
     // Maps to each neighbour rank an array of WorldVectors. This array contain the 
     // coordinates of all dofs this rank shares on the interior boundary with the 
     // neighbour rank. A rank sends the coordinates to another rank, if it owns the
@@ -1662,13 +1511,6 @@ namespace AMDiS {
 	bool b = mesh->getDofIndexCoords(*dofIt, feSpace, coords);
 	TEST_EXIT(b)("Cannot find DOF in mesh!\n");
 
-#if 0
-	if (mpiRank == 3 && it->first == 2) {
-	  std::cout << "SEND COORDS: " << *dofIt << " = " << **dofIt << std::endl;
-	  coords.print();
-	}
-#endif
-
 	sendCoords[it->first].push_back(coords);
       }
     }
@@ -1680,14 +1522,6 @@ namespace AMDiS {
 	bool b = mesh->getDofIndexCoords(*dofIt, feSpace, coords);
 	TEST_EXIT(b)("Cannot find DOF in mesh!\n");
 	recvCoords[it->first].push_back(coords);
-
-#if 0
-	if (mpiRank == 2 && it->first == 3) {
-	  std::cout << "RECV COORDS: " << *dofIt << " = " << **dofIt << std::endl;
-	  coords.print();
-	}
-#endif
-
       }
     }
 
diff --git a/AMDiS/src/ParallelDomainVec.cc b/AMDiS/src/ParallelDomainVec.cc
index c2a127ec..5416c468 100644
--- a/AMDiS/src/ParallelDomainVec.cc
+++ b/AMDiS/src/ParallelDomainVec.cc
@@ -66,7 +66,7 @@ namespace AMDiS {
 #else
     INFO(info, 8)("solution of discrete system needed %.5f seconds\n",
 		   TIME_USED(first, clock()));
-#endif
+#endif    
   }
 
 }
diff --git a/AMDiS/src/ProblemVec.cc b/AMDiS/src/ProblemVec.cc
index 39fcd144..bdbea9e7 100644
--- a/AMDiS/src/ProblemVec.cc
+++ b/AMDiS/src/ProblemVec.cc
@@ -666,6 +666,9 @@ namespace AMDiS {
 
     traverseInfo.updateStatus();
 
+    // Used to calculate the overall number of non zero entries.
+    int nnz = 0;
+
     for (int i = 0; i < nComponents; i++) {
       for (int j = 0; j < nComponents; j++) {
 
@@ -687,9 +690,8 @@ namespace AMDiS {
 	// If the matrix should not be assembled, the rhs vector has to be considered.
 	// This will be only done, if i == j. So, if both is not true, we can jump
 	// to the next matrix.
-	if (!assembleMatrix && i != j) {
+	if (!assembleMatrix && i != j)
 	  continue;
-	}
 
 	if (assembleMatrix && matrix->getBoundaryManager())
 	  matrix->getBoundaryManager()->initMatrix(matrix);
@@ -759,6 +761,12 @@ namespace AMDiS {
  	  matrix->getBoundaryManager()->exitMatrix(matrix);	  
 	
 	assembledMatrix[i][j] = true;
+
+	if (assembleMatrix)
+	  matrix->finishInsertion();
+	
+	if (matrix)
+	  nnz += matrix->getBaseMatrix().nnz();
       }
 
       // And now assemble boundary conditions on the vectors
@@ -768,16 +776,6 @@ namespace AMDiS {
 				 assembleFlag);      
     }
 
-    int nnz = 0;
-
-    // Finish insertion
-    for (int i = 0; i < nComponents; i++) 
-      for (int j = 0; j < nComponents; j++) 
- 	if ((*systemMatrix)[i][j]) {
- 	  (*systemMatrix)[i][j]->finishInsertion(); 
-	  nnz += (*systemMatrix)[i][j]->getBaseMatrix().nnz();
-	}    
-
     solverMatrix.setMatrix(*systemMatrix);
 
     createPrecon();
-- 
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